This is always hard. The old Vinyl mat they used to make would expand and contract like crazy making it hard to keep a good fit. I remember installing it once on a Bronco, outside on a spring CA morning, by late afternoon it was about 2" bigger in places that fit great in the morning.
The new parchment rubber mat is lots of fun to play with too, but harder to manipulate fit with. I've done 3 so far, stock restos, so no underlayment, fuzzy stuff. All that just adds to the height and fitment issues in my opinion. Down to race anyone who has it too as my acc pedal has 2" more down travel...
Anyway, I start with the fuel valve to get that area by the driver seat sucked up to the wall and keep it from moving anywhere else. I feel it's molded too tight around tunnel to floor, and even copious amounts of heat from a heat gun doesn't allow it to sit down in those areas all the way. have to pick a happy medium there with reference to the kickpanels.
Now, Maybe the underlayment only on the floor area would remedy this? In any case, install in as warm as possible weather as you can, and take lots of time, and dont start trimming immediately, which means you may have to leave your doors open for a week or two.